We have begun curating quantitative MS2 datasets into PSP: these will be accessible from the “QUANT”
column in the Browsing interfaces as shown below. The CST-LINCS datasets described below are new
datasets not yet published elsewhere. They are made available to the community so that novel analytical
tools might be applied to the multidimensional data that will lead to new insights in network biology
and the cell biology of cancer.

CST-LINCS MS TMT Data.

PTM-specific antibodies were used to enrich modified peptides followed by 6-plex TMT mass-spec analyses
to quantitatively measure over 12,000 differentially phosphorylated, acetylated, and methylated sites on
over 4,000 proteins. Two sets of experiments were performed:

The “Lung Cancer Cell Line” (LCCL) study includes 45 lung cancer cell lines, 12 SCLC and
33 NSCLC cell lines, including those with known oncogenic kinases and fusion-proteins. Comparison of
NSCLC with SCLC reveals different kinase signatures between the two types.

The “Drug Treament” (TKI) study includes 6 cancer cell lines with known disease drivers,
5 NSCLC and one gastric carcinoma with an amplification of the Met oncogene. Cell lines were treated
with three different TKIs and the kinetics of protein modifications were followed from 1 to 24
hours. These datasets are available in the accompanying Excel file.